Sodium in PDB 8pz0: Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.
Enzymatic activity of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.
All present enzymatic activity of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.:
3.4.11.1;
3.4.11.10;
Protein crystallography data
The structure of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14., PDB code: 8pz0
was solved by
M.C.Simpson,
C.M.Czekster,
C.J.Harding,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.49 /
1.80
|
Space group
|
P 63 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.95,
181.95,
87.43,
90,
90,
120
|
R / Rfree (%)
|
16.8 /
19
|
Other elements in 8pz0:
The structure of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.
(pdb code 8pz0). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14., PDB code: 8pz0:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 8pz0
Go back to
Sodium Binding Sites List in 8pz0
Sodium binding site 1 out
of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na606
b:32.6
occ:1.00
|
OD2
|
A:ASP310
|
1.8
|
50.2
|
1.0
|
O
|
A:HOH749
|
2.1
|
53.9
|
1.0
|
OE2
|
A:GLU371
|
2.1
|
47.0
|
1.0
|
NZ
|
A:LYS287
|
2.3
|
53.8
|
1.0
|
OD2
|
A:ASP292
|
2.5
|
42.0
|
1.0
|
CG
|
A:ASP310
|
2.7
|
56.9
|
1.0
|
OD1
|
A:ASP310
|
3.1
|
48.0
|
1.0
|
CD
|
A:GLU371
|
3.1
|
42.3
|
1.0
|
NA
|
A:NA610
|
3.2
|
40.8
|
1.0
|
CE
|
A:LYS287
|
3.2
|
42.7
|
1.0
|
CG
|
A:ASP292
|
3.3
|
46.3
|
1.0
|
OE1
|
A:GLU371
|
3.5
|
49.0
|
1.0
|
O2
|
A:BCT605
|
3.7
|
53.7
|
1.0
|
CB
|
A:ASP292
|
3.8
|
42.2
|
1.0
|
CB
|
A:ASP310
|
4.1
|
40.2
|
1.0
|
OD1
|
A:ASP292
|
4.3
|
42.4
|
1.0
|
O
|
A:THR396
|
4.3
|
38.9
|
1.0
|
CG
|
A:GLU371
|
4.5
|
43.2
|
1.0
|
CG2
|
A:ILE289
|
4.5
|
37.2
|
1.0
|
CB
|
A:ILE289
|
4.5
|
34.8
|
1.0
|
CG1
|
A:ILE289
|
4.6
|
38.1
|
1.0
|
CD
|
A:LYS287
|
4.6
|
37.9
|
1.0
|
N
|
A:GLY372
|
4.6
|
41.0
|
1.0
|
O
|
A:ASP369
|
4.8
|
41.4
|
1.0
|
C
|
A:BCT605
|
4.9
|
54.5
|
1.0
|
CA
|
A:GLY372
|
4.9
|
44.1
|
1.0
|
|
Sodium binding site 2 out
of 5 in 8pz0
Go back to
Sodium Binding Sites List in 8pz0
Sodium binding site 2 out
of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na607
b:63.0
occ:1.00
|
N
|
A:GLU102
|
2.9
|
54.9
|
1.0
|
O
|
A:ALA99
|
2.9
|
44.1
|
1.0
|
CB
|
A:GLU102
|
3.2
|
60.7
|
1.0
|
N
|
A:LYS101
|
3.3
|
47.6
|
1.0
|
CD2
|
A:LEU105
|
3.3
|
50.3
|
1.0
|
C
|
A:GLY100
|
3.4
|
47.3
|
1.0
|
CA
|
A:GLU102
|
3.5
|
62.4
|
1.0
|
CA
|
A:GLY100
|
3.5
|
43.0
|
1.0
|
O
|
A:HOH994
|
3.6
|
55.7
|
1.0
|
O
|
A:GLU102
|
3.7
|
61.1
|
1.0
|
CG
|
A:GLU102
|
3.7
|
66.5
|
1.0
|
C
|
A:ALA99
|
3.9
|
43.0
|
1.0
|
C
|
A:LYS101
|
3.9
|
58.0
|
1.0
|
C
|
A:GLU102
|
4.0
|
64.9
|
1.0
|
NE2
|
A:GLN109
|
4.1
|
66.2
|
1.0
|
O
|
A:GLY100
|
4.1
|
49.2
|
1.0
|
CA
|
A:LYS101
|
4.2
|
57.5
|
1.0
|
N
|
A:GLY100
|
4.2
|
41.7
|
1.0
|
CG2
|
A:VAL77
|
4.5
|
42.6
|
1.0
|
CG
|
A:LEU105
|
4.6
|
46.8
|
1.0
|
O
|
A:GLU104
|
4.7
|
50.0
|
1.0
|
CD
|
A:GLN109
|
4.7
|
60.6
|
1.0
|
OE1
|
A:GLN109
|
4.8
|
58.1
|
1.0
|
NH2
|
A:ARG47
|
4.9
|
64.8
|
1.0
|
CD
|
A:GLU102
|
4.9
|
74.6
|
1.0
|
O
|
A:LYS101
|
5.0
|
59.8
|
1.0
|
|
Sodium binding site 3 out
of 5 in 8pz0
Go back to
Sodium Binding Sites List in 8pz0
Sodium binding site 3 out
of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na608
b:63.4
occ:1.00
|
CG
|
A:GLN109
|
2.9
|
44.1
|
1.0
|
N
|
A:GLN109
|
3.0
|
38.5
|
1.0
|
OE1
|
A:GLN109
|
3.1
|
58.1
|
1.0
|
CA
|
A:GLY106
|
3.2
|
44.9
|
1.0
|
CD
|
A:GLN109
|
3.3
|
60.6
|
1.0
|
C
|
A:GLY106
|
3.4
|
47.9
|
1.0
|
N
|
A:GLY106
|
3.4
|
42.0
|
1.0
|
O
|
A:HOH939
|
3.4
|
60.8
|
1.0
|
CB
|
A:GLN109
|
3.4
|
39.8
|
1.0
|
O
|
A:GLY106
|
3.5
|
42.3
|
1.0
|
N
|
A:ARG108
|
3.7
|
38.9
|
1.0
|
CA
|
A:GLN109
|
3.8
|
39.5
|
1.0
|
CB
|
A:ARG108
|
3.8
|
43.0
|
1.0
|
C
|
A:ARG108
|
3.9
|
39.8
|
1.0
|
CA
|
A:ARG108
|
4.0
|
44.0
|
1.0
|
N
|
A:ASP107
|
4.1
|
43.4
|
1.0
|
NE2
|
A:GLN109
|
4.5
|
66.2
|
1.0
|
C
|
A:ASP107
|
4.5
|
44.5
|
1.0
|
C
|
A:LEU105
|
4.7
|
45.4
|
1.0
|
CA
|
A:ASP107
|
4.9
|
45.0
|
1.0
|
|
Sodium binding site 4 out
of 5 in 8pz0
Go back to
Sodium Binding Sites List in 8pz0
Sodium binding site 4 out
of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na609
b:57.7
occ:1.00
|
CA
|
A:GLY459
|
2.7
|
55.1
|
1.0
|
OE1
|
A:GLN446
|
2.8
|
50.0
|
1.0
|
C
|
A:GLY459
|
3.0
|
45.4
|
1.0
|
N
|
A:LYS461
|
3.0
|
44.2
|
1.0
|
N
|
A:GLY459
|
3.1
|
59.4
|
1.0
|
N
|
A:PRO460
|
3.2
|
43.8
|
1.0
|
CD
|
A:PRO460
|
3.4
|
50.7
|
1.0
|
CB
|
A:LYS461
|
3.5
|
42.1
|
1.0
|
CG
|
A:LYS461
|
3.6
|
47.1
|
1.0
|
CA
|
A:LYS461
|
3.7
|
44.1
|
1.0
|
O
|
A:GLY459
|
3.7
|
46.0
|
1.0
|
O
|
A:LYS461
|
3.8
|
39.6
|
1.0
|
CD
|
A:GLN446
|
3.8
|
51.4
|
1.0
|
C
|
A:PRO460
|
4.0
|
45.2
|
1.0
|
CA
|
A:PRO460
|
4.2
|
46.6
|
1.0
|
C
|
A:LYS461
|
4.2
|
40.1
|
1.0
|
CD
|
A:LYS461
|
4.3
|
46.3
|
1.0
|
O
|
A:HOH753
|
4.3
|
41.4
|
1.0
|
CG
|
A:PRO460
|
4.4
|
52.8
|
1.0
|
C
|
A:GLY458
|
4.4
|
55.4
|
1.0
|
NE2
|
A:GLN446
|
4.4
|
52.0
|
1.0
|
CG
|
A:GLN446
|
4.8
|
45.5
|
1.0
|
|
Sodium binding site 5 out
of 5 in 8pz0
Go back to
Sodium Binding Sites List in 8pz0
Sodium binding site 5 out
of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na610
b:40.8
occ:1.00
|
OD1
|
A:ASP369
|
2.1
|
45.2
|
1.0
|
OD2
|
A:ASP292
|
2.1
|
42.0
|
1.0
|
O
|
A:ASP369
|
2.1
|
41.4
|
1.0
|
OE1
|
A:GLU371
|
2.2
|
49.0
|
1.0
|
O
|
A:HOH749
|
2.2
|
53.9
|
1.0
|
CG
|
A:ASP292
|
3.0
|
46.3
|
1.0
|
C
|
A:ASP369
|
3.0
|
42.1
|
1.0
|
CG
|
A:ASP369
|
3.1
|
47.3
|
1.0
|
CD
|
A:GLU371
|
3.1
|
42.3
|
1.0
|
NA
|
A:NA606
|
3.2
|
32.6
|
1.0
|
OD1
|
A:ASP292
|
3.3
|
42.4
|
1.0
|
OE2
|
A:GLU371
|
3.4
|
47.0
|
1.0
|
CA
|
A:ASP369
|
3.5
|
40.9
|
1.0
|
NZ
|
A:LYS299
|
3.8
|
47.4
|
1.0
|
CB
|
A:ASP369
|
3.9
|
41.5
|
1.0
|
O2
|
A:BCT605
|
3.9
|
53.7
|
1.0
|
OD2
|
A:ASP369
|
4.0
|
49.0
|
1.0
|
CE
|
A:LYS299
|
4.1
|
44.3
|
1.0
|
N
|
A:ALA370
|
4.2
|
38.2
|
1.0
|
N
|
A:GLU371
|
4.3
|
40.6
|
1.0
|
CB
|
A:ASP292
|
4.4
|
42.2
|
1.0
|
CG
|
A:GLU371
|
4.5
|
43.2
|
1.0
|
OD2
|
A:ASP310
|
4.6
|
50.2
|
1.0
|
CA
|
A:ALA370
|
4.6
|
40.3
|
1.0
|
C
|
A:BCT605
|
4.7
|
54.5
|
1.0
|
ND2
|
A:ASN342
|
4.7
|
41.0
|
1.0
|
CA
|
A:GLY294
|
4.8
|
41.5
|
1.0
|
N
|
A:ASP369
|
4.9
|
38.1
|
1.0
|
CB
|
A:GLU371
|
4.9
|
44.0
|
1.0
|
|
Reference:
M.C.Simpson,
C.J.Harding,
R.M.Czekster,
L.Remmel,
B.E.Bode,
C.M.Czekster.
Unveiling the Catalytic Mechanism of A Processive Metalloaminopeptidase. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37924287
DOI: 10.1021/ACS.BIOCHEM.3C00420
Page generated: Wed Oct 9 13:05:13 2024
|